rs7075141

chr10-1045255-G-Achr10-1045255-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004508.4(IDI1):c.141-1084C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 152,230 control chromosomes in the GnomAD database, including 33,802 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.66 (33802 hom., cov: 35)
• Consequence: IDI1 NM_004508.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

Genes affected

IDI1 (HGNC:5387): (isopentenyl-diphosphate delta isomerase 1) IDI1 encodes a peroxisomally-localized enzyme that catalyzes the interconversion of isopentenyl diphosphate (IPP) to its highly electrophilic isomer, dimethylallyl diphosphate (DMAPP), which are the substrates for the successive reaction that results in the synthesis of farnesyl diphosphate and, ultimately, cholesterol. It has been shown in peroxisomal deficiency diseases such as Zellweger syndrome and neonatal adrenoleukodystrophy that there is reduction in IPP isomerase activity. [provided by RefSeq, Jul 2008]

IDI2-AS1 (HGNC:30885): (IDI2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IDI1	NM_004508.4	c.141-1084C>T		intron_variant		ENST00000381344.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IDI1	ENST00000381344.8	c.141-1084C>T		intron_variant		1	NM_004508.4
IDI2-AS1	ENST00000665330.1	n.1979G>A		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100252 AN: 152112 Hom.: 33752 Cov.: 35

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.646

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.659 AC: 100354 AN: 152230 Hom.: 33802 Cov.: 35 AF XY: 0.670 AC XY: 49850 AN XY: 74436

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.715

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.806

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.650

Alfa AF: 0.683 Hom.: 20227

Bravo AF: 0.645

Asia WGS AF: 0.764 AC: 2655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.54
Dann	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7075141; hg19: chr10-1091195;